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"Captain's log: Stardate 5501.2. We are orbiting the planetLactra VII. Our mission is to discover the whereabouts or fate of a six member science crew. Voice contact having yielded nothing, a landing party beamed aboard to see if the deserted ship's log and computers could give us any information."

Their computer intones, "It is now 32 minutes since our last contact with the three members of our crew on the planet's surface. As the senior officer aboard I, Lieutenant CommanderMarkel, have made the following decision. The three remaining crew members, myself included, will beam down to effect a rescue. If for any reason we do not return, be it known that..." Kirk cuts off the log and says, "It was against all orders." McCoy claims, "The crew was apparently desperate." Kirk states, "The captain of a ship, no matter his rank, must follow the book." Spock remarks, "A capability, I'm afraid, out of the reach of most Humans." Kirk wants a landing party to beam down to the last known coordinates the crew used. "Gentlemen, we'll travel light. Phasers, tricorders, communicators and medical kit."

Their communicator picks up a short signal, but there is no trace of sentient inhabitants. They are attacked by a beast that seems similar to one on Canopus III, which is light years away, but the desert area they now occupy is the same. As they continue walking the environment changes. Spock doesn't think that two such disparate ecologies could co-exist so closely. Scott communicates that ship's sensors have discovered a large concentration of lifeforms 98.5 kilometers north east. Apparently a city or central gathering place. Spock's has a theory that they have found a plethora of different habitats and their inhabitants. The various environments have been manufactured, not created by nature.

They are attacked by other creatures, but before any harm can befall them the creatures are stopped by a force field. The crew meets the Lactrans, a group of twenty-foot slugs who capture them. Spock discovers the Lactrans are telepathic, but the speed at which their thoughts flow is too difficult for him to comprehend, except for the most fleeting image. He realizes that they are advanced as much beyond Kirk as he is to a colony of ants. They are taken to an environment like Earth and imprisoned along with the three remaining Arielcrewmembers. They have become exhibits in a zoo.

The Lactrans are unaware Ariel's LieutenantRandolph has become ill, and they were too late to save the first landing party. They have tried every means of escape they could. They have attempted communication but only aroused a quivering motion. Kirk asks Spock to try to make contact but he can't. His impression is that they are laughing at him. They all concentrate their need to have McCoy's medical kit that is located outside a force field and succeed.

Spock notices that the Lactrans can pick up specific thought transmissions from them if they care to go to the trouble. He suggests that one of them should appear to be ill and the rest of them should put strong thoughts in their minds that a communicator is needed for recovery. A child responds, gives them the communicator and Kirk contacts the ship. They are beamed up along with the child. The elders are worried about the child and think Kirk made the child disappear. The child's parents are worried and almost kill Kirk in an attempt to contact him. On the starship, the child reads Scott's brain, all the information contained in the library computer and sends the Enterprise flying out of orbit. Scotty convinced the child that Humans are not pets and to return and let his parents know what he has learned. The child does so and the Lactrans release the crew from confinement and allow them to leave because the Lactrans do not feel the crew belongs in their zoo. They send a final telepathic message to Spock – "Humans may return when they grow up, in 20 or 30 of their centuries and it will take Spock some time to figure out how long that is to them." Kirk says, "Either way Mr. Spock, it will hardly be our problem."

"You Vulcans are the most impossible, unimaginative..."
"Bones, that's not helping the situation."
"Sorry, Jim."

- McCoy begins to hurl insults at Spock but Kirk stops him

"Jim, if the others are lost, why take the risk?"
"Because they may not be dead. We have to find out."
"It's still a risk."
"That's why we're here, Bones."

- McCoy and Kirk

"My shoes are full of sand."
"Doctor, your lack of scientific interest is amazing."
"I'll be happy to discuss that with you, Mr. Spock, next time you drop in to my medical lab."

- McCoy and Spock

"They don't seem very interested in communicating with us, if they can communicate at all."
"Perhaps not in a way we understand. I keep receiving impressions."
"Any ideas, doctor?"
"Well, I've got one and I definitely don't like it. I'd guess they're doing exactly what we would do."
"Which is?"
"Well, if we came upon an alien creature we'd never seen before, the first thing we'd do is to make sure it was free of harmful bacteria. Then we'd see if it was intelligent."
"Congratulations, Doctor. A most logical assumption."

- McCoy, Spock and Kirk

"Are the aliens telepathic?"
"I've come to the conclusion they are, captain, but the speed at which the thoughts flow is too great for me to comprehend, except for the most fleeting image."
"Surely we can communicate with them someway."
"They appear to be as advanced beyond Earth civilization as you are from a colony of ants."

- Kirk and Spock

"We are considered simplistic, but in the process of evolving into a higher order."
"Even Vulcans?"
"Yes. Even Vulcans."

The text commentary for this episode, written by Michael and Denise Okuda, speculates, "Like many animated Star Trek episodes, 'The Eye of the Beholder' could easily have been an episode of the original series. Assuming, of course, that the original series could have afforded the sets and the effects." These elements would actually not have been possible, though, for the original Star Trek, as the text commentary explains. "[The] sea creature [near the start of this episode] illustrates the advantage of animation over traditional live-action filmmaking. It would have been very difficult for the original Star Trek to afford such a creature [....] The slug-like Lactrans are far beyond anything that would have been attempted on the original series. Similarly, the other animals and [the Lactran city's elaborately] futuristic architecture would all have been beyond the resources of the original series [....] [The Lactrans' tentacle-like] snouts would have been a significant challenge if attempted in live-action puppetry."

The episode's text commentary implies that the effect of both the landing party from the Enterprise beaming to Lactra VII and steam that can be seen rising from a marshy lake upon the group's reintegration were classed as special animation effects and, as such, were included in the purview of Reuben Timmins.

The shots of the Enterprise that are shown when Kirk contacts the vessel were an economical measure, as they lessened the amount of character animation that had to be created for the installment. Another such measure was the fact that the Maravel dragons that attack the Enterprise landing party used a recycled character design that appear as the Swoopers in the earlier TAS installment "The Infinite Vulcan" and are seen again as the mechanical sentinels in the episode following this one, "The Jihad". These cost-cutting measures enabled Filmation to concentrate on the unique designs needed for this episode, such as the Lactrans and their city. (TAS DVD text commentary)

The design of the Lactrans was well-suited to animation. For example, their mode of travel was very economical, since the animators did not need to illustrate moving feet, and the large eyes of the aliens proved an effective means of conveying emotion without dialogue, thereby helping to minimize not only the quantity of lip movements that had to be drawn and synced with the speaking in the episode's soundtrack but also the amount of dialogue that had to be recorded for the episode. The Lactrans' snouts did require a considerable number of drawings, but only when they were moving. (TAS DVD text commentary)

Kirk's response to McCoy worrying about the risk involved in the captain's plan of beaming a landing party to the last known coordinates of the USS Ariel's crew (specifically, "That's why we're here") is a subtle reference to a well-known speech that Kirk makes in TOS: "Return to Tomorrow", wherein he says, "Risk is our business."

The predicament that the captured Starfleet officers find themselves in (i.e., being confined to the Lactra VII zoo) is similar to a situation in which Captain Christopher Pike finds himself, in TOS: "The Cage" (wherein Talosians are the zookeepers).

This is the third of three times in Star Trek: The Animated Series when the character of Arex does not appear. He also does not feature in "Yesteryear" and "The Slaver Weapon".

This is also one of three TAS episodes in which the character of Uhura does not appear, other such outings being "Yesteryear" and "The Jihad".

David P. Harmon was dissatisfied with this episode, later remarking, "I wasn't that happy with it." He went on to relate that this was because he didn't believe animation, which disappointed him generally, was suitable for the emotional depth of Star Trek. (Starlog issue #117, p. 44)

The editors of Trek magazine collectively scored this episode 3 out of 5 stars (a rating that they termed "good"). (The Best of Trek #1, p. 111)

In The Star Trek Files magazine, John Peel commented, "A pretty straight-forward story that works quite well, despite the obviousness of the plot. The idea of the Lactrans being so advanced that they do not recognize the crew as intelligent seems a little far-fetched, but it isn't impossible, I suppose. One thing that puzzles me about the story is the logic of it, however." In particular, Peel struggled with the plot point that three crew members from the USS Ariel had beamed down in search of a lost landing party, leaving the vessel unoccupied. "Aside from the fact (as Kirk points out) that this is against Starfleet regulations," said Peel, "one thing occurs to me – how did they expect to return to their ship, since there is no-one up there to manipulate the transporter? It couldn't work on automatic, since they would have moved from their original beam-down point. It seems like a very silly error to make." (The Star Trek Files: The Animated Voyages End, pp. 26-28)